I don't think the demographics of Mexico in that time period are very well documented (though there have been a (very) wide range of estimates).

This source: The Peopling of Mexico from Origins to Revolution by Robert McCaa

http://www.hist.umn.edu/~rmccaa/mxpoprev/cambridg3.htm

Is by an Academic, in 1997, estimating that the bottom of the demographic trough in Mexico after the Columbian Exchange, was in about 1650, and he cites a number of population estimates (for the indigenous population at this point (between 1.2 and 3.4m) and for the pre-exchange population (between 5 and 25m)).

I don't know his reputation, or how accurate some of these estimates are, but this might give you a place to start, and his sources might give you further information.